We tested presence and organization of Gymny in species representing a range of genome sizes [1], [44] [46] across three monophyletic lineages within the genus Pinus, and other gymnosperms (Table 4) using probes derived from overlapping internal regions of RLG_Gymny_EU912388-1 (Southern probes Fr1035 and Fr1075, Figure 1).
An assembly derived from overlapping EST and FL-cDNA alignments can contain more than one event.
For each taxon in our analysis, a set of clusters consisting of contigs derived from overlapping reads was obtained.
Since cDNA sequences are often truncated, we used consensus exon-intron structures derived from overlapping and similar cDNA mappings.
Sequences were also derived from overlapping PCR fragments as previously described [ 12] (see additional fig. 1, 2, 3).
This method is base on the branch stability in the bootstrap trees derived from overlapping input sets of genome-wide miRNA precursor sequences.
In our method, the families are identified based on branch stability in the bootstrap trees derived from overlapping input sets of genome-wide miRNA precursor sequences.
That map was routinely verified with independent data, including sequence derived from overlapping BACs, alignments with orthologous sequence from another species, and/or results of PCR-based experiments to confirm contig adjacency.
In this study, we designed an analysis pipeline (the Phylogeny-Bootstrap-Cluster (PBC) pipeline) to identify miRNA families based on branch stability in the bootstrap trees derived from overlapping genome-wide miRNA sequence sets.
The biomarker results indicate that PFS and OS benefit in patients with high EGFR gene copy number in their tumours appears to be derived from overlapping EGFR mutation positivity.
From a statistical point of view these tests are not entirely rigorous, as they do not take into account the inter-dependence between the data points derived from overlapping pairs of species.
